differentially expression analysis using raw read counts

Question

[ashkan]

I have raw read count from RNA-seq(meaning I aligned fastq files and got raw read counts using HTSeq). is there any way to do differentially expression analysis to identify DEGs? thanks

[Farbod]

Hi Ashkan,

Please have a look here and here.

~ Best

[zizigolu]

this tutorial is very useful

C: DE analysis by edgeR

Answer 1

[WouterDeCoster]

Have a look at DESeq2, edgeR, limma-voom and perhaps this workflow from Bioconductor http://www.bioconductor.org/help/workflows/rnaseqGene/

Answer 2

[Ron]

Here is tutorial using DESEQ2

https://www.r-bloggers.com/tutorial-rna-seq-differential-expression-pathway-analysis-with-sailfish-deseq2-gage-and-pathview/